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x-ray structure of NeoB from streptomyces fradiae in complex with PLP and neomycin (as the external aldimine) at pH 9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CBK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 18-20% PEG-3350, 100 mM MgCl2, 100 mM CHES, 1 mMPLP, 5 mM neomycin
Crystal Properties Matthews coefficient Solvent content 2.31 46.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.742 α = 69.58 b = 59.153 β = 77.62 c = 70.313 γ = 78.45
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD Bruker Platinum 135 2017-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.65 50 94.5 0.06 0.06 10.6 3 95942
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.75 86.2 0.248 0.248 2.7 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6cbk 1.65 50 91161 4781 94.51 0.16298 0.16118 0.1732 0.19805 0.2066 RANDOM 20.079
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.22 -0.54 -0.68 -0.58 0.47 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.919 r_dihedral_angle_4_deg 16.504 r_dihedral_angle_3_deg 15.078 r_long_range_B_refined 6.668 r_long_range_B_other 6.668 r_dihedral_angle_1_deg 6.426 r_scangle_other 5.4 r_scbond_it 3.77 r_scbond_other 3.77 r_mcangle_other 2.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.919 r_dihedral_angle_4_deg 16.504 r_dihedral_angle_3_deg 15.078 r_long_range_B_refined 6.668 r_long_range_B_other 6.668 r_dihedral_angle_1_deg 6.426 r_scangle_other 5.4 r_scbond_it 3.77 r_scbond_other 3.77 r_mcangle_other 2.865 r_mcangle_it 2.864 r_mcbond_it 2.263 r_mcbond_other 2.26 r_angle_refined_deg 1.6 r_angle_other_deg 0.812 r_chiral_restr 0.11 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6192 Nucleic Acid Atoms Solvent Atoms 808 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing